Apple has issued a statement to The Register confirming reports and rumors stating that iOS web apps and embedded web views in iOS applications are throttled and run twice as slow as Safari.

iOS 4.3 includes a new “nitro” web processing engine, which promises to run java script twice as fast as earlier versions of iOS Safari. According to Apple’s iOS feature page:

As you surf the web, your fingers will love the responsiveness of the new Nitro JavaScript engine powering Safari. It runs JavaScript up to twice as fast as in iOS 4.2.2Which means you get more speed behind each page load. And sites with lots of interactive features can appear on your screen even faster.

The only affected users would be users of third-party web browsers that utilize the web engine that Apple provides to developers in Xcode. Full-screen web applications that launch from the iOS homescreen are, of course, affected as well.

We presume that Apple has left out asynchronous mode of execution and other HTML5 goodies, too.

Apple spokesperson Trudy Miller confirms:

The embedded web viewer does not take advantage of Safari’s web performance optimizations.

Apple does not provide a reason as to why this is the case but here is our speculation from the other day:

Of course, Apple has a vested interest in native apps due to a 30 percent cut they take from sales. I’ve argued nearly two years ago that the web is the ultimate app store and it’s true that many native apps are easily replicated with HTML/CSS, especially the stuff like news readers, social networking clients and more. Also important, web apps run on any device with a standards-complaint browser whereas their native counterparts lock you into a specific mobile platform.